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- PDB-5vc3: CRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH BOS... -

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Basic information

Entry
Database: PDB / ID: 5vc3
TitleCRYSTAL STRUCTURE OF HUMAN WEE1 KINASE DOMAIN IN COMPLEX WITH BOSUTINIB
ComponentsWee1-like protein kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / CELL CYCLE / WEE1 / TRANSFERASE / INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis ...G2/M DNA replication checkpoint / negative regulation of G2/M transition of mitotic cell cycle / Polo-like kinase mediated events / negative regulation of G1/S transition of mitotic cell cycle / establishment of cell polarity / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / neuron projection morphogenesis / positive regulation of DNA replication / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / microtubule cytoskeleton organization / G2/M transition of mitotic cell cycle / Factors involved in megakaryocyte development and platelet production / protein tyrosine kinase activity / cell division / nucleolus / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytoplasm
Similarity search - Function
Wee1-like protein kinase / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Wee1-like protein kinase / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DB8 / Wee1-like protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.97 Å
AuthorsZhu, J.-Y. / Schonbrunn, E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)UO1 HD076542 United States
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors.
Authors: Zhu, J.Y. / Cuellar, R.A. / Berndt, N. / Lee, H.E. / Olesen, S.H. / Martin, M.P. / Jensen, J.T. / Georg, G.I. / Schonbrunn, E.
History
DepositionMar 30, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 23, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Wee1-like protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2557
Polymers32,4411
Non-polymers8146
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.520, 45.230, 60.440
Angle α, β, γ (deg.)90.000, 102.430, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Wee1-like protein kinase / WEE1hu / Wee1A kinase


Mass: 32440.900 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 291-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: WEE1 / Plasmid: pET28a / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIPL
References: UniProt: P30291, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-DB8 / 4-[(2,4-dichloro-5-methoxyphenyl)amino]-6-methoxy-7-[3-(4-methylpiperazin-1-yl)propoxy]quinoline-3-carbonitrile / Bosutinib


Mass: 530.446 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H29Cl2N5O3 / Comment: medication*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 5.0 MG/ML WEE1, 25 mM Na/K phosphate, 1 mM DTT, 0.05 M ammonium sulfate, 0.05 M Bis-tris (pH 5.5),7.5 % PEG 3350, 1 mM Bosutinib

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 2, 2016 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→59.024 Å / Num. obs: 20512 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.635 % / Biso Wilson estimate: 29.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.068 / Χ2: 1.01 / Net I/σ(I): 12.46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.9-1.953.5670.3533.7615020.860.41594.8
1.95-23.6840.3144.5314350.8760.36895.8
2-2.063.6870.2385.3514110.9350.27895.5
2.06-2.123.720.1866.2413880.9620.21896
2.12-2.193.7260.1497.1113290.9820.17496.4
2.19-2.273.7340.1437.2412880.9820.16795.3
2.27-2.363.7270.1298.0112600.9860.15196.9
2.36-2.453.7060.1049.3712160.9920.12297.7
2.45-2.563.7140.09510.2511570.9940.11296.6
2.56-2.693.6580.08811.9411460.9930.10397.6
2.69-2.833.560.08114.1610470.9930.09696.9
2.83-33.3560.06918.9410060.9890.08296.6
3-3.213.4720.05922.579550.9910.0797.1
3.21-3.473.5440.05421.998820.9940.06396.8
3.47-3.83.6120.04123.578190.9980.04897.8
3.8-4.253.5990.0424.417630.9960.04799.1
4.25-4.913.6050.03525.466550.9980.04198.2
4.91-6.013.6280.03425.155720.9980.0499.7
6.01-8.53.590.0325.94580.9980.03698.7
8.5-59.0243.4080.02526.182230.9970.03186.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V5Y

5v5y


Resolution: 1.97→59.024 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 28.3
RfactorNum. reflection% reflection
Rfree0.2536 927 5 %
Rwork0.212 --
obs-18523 97.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 209.02 Å2 / Biso mean: 50.2264 Å2 / Biso min: 17.38 Å2
Refinement stepCycle: final / Resolution: 1.97→59.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 106 72 2249
Biso mean--54.05 35.64 -
Num. residues----260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062166
X-RAY DIFFRACTIONf_angle_d0.9482916
X-RAY DIFFRACTIONf_chiral_restr0.034313
X-RAY DIFFRACTIONf_plane_restr0.004371
X-RAY DIFFRACTIONf_dihedral_angle_d15.04811
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9701-2.0740.30351300.27482457258796
2.074-2.2040.30161300.25352470260096
2.204-2.37410.26461300.24712471260196
2.3741-2.61310.29421320.24452507263997
2.6131-2.99120.25681320.23122522265497
2.9912-3.76850.25911360.19932573270999
3.7685-59.05040.20681370.17652596273398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.9059-0.5595-0.52792.22950.82734.937-0.10150.3309-0.298-0.11960.09770.1212-0.0187-0.21590.00130.1711-0.0121-0.01890.24970.00920.2964-11.0105-2.39997.2668
21.49160.05550.87410.9075-0.44541.49930.3957-0.1149-1.0053-0.63680.15340.06160.39530.45911.552-0.26630.10260.05910.2697-0.10250.363-6.6187-6.96299.4907
35.00841.08150.87292.91320.01851.76920.02440.12240.0761-0.12730.023-0.04730.06890.0057-0.0490.13220.03580.0290.23490.01610.2562-0.4861.63713.6749
45.42530.005-0.29963.3950.61622.2020.5113-1.55330.92030.7716-0.55560.3633-0.205-0.3076-0.53070.1915-0.09110.05010.6765-0.13910.21427.43269.93325.4556
51.85350.45990.26152.583-0.7642.0370.2303-0.59430.05970.2703-0.26590.2085-0.1597-0.2171-0.18870.18680.00490.02570.319-0.04720.24472.9747.005718.2828
61.6018-1.23920.87962.671-0.38420.9648-0.23830.5351-0.7956-0.5774-0.1938-0.15861.0060.0951-0.04030.11180.18940.03670.18980.08470.322614.5582-1.314513.4806
72.91241.4142-0.30951.5030.23432.27710.12310.1470.6107-0.2603-0.2451-0.4606-0.33620.1339-0.68120.1558-0.02780.0650.26270.14080.324219.235810.134911.9805
81.1142-1.5766-0.16784.6736-1.23910.8298-0.036-0.37131.91730.15540.0803-0.8067-0.38160.3368-0.16360.3129-0.060.0010.3732-0.07670.800117.416322.336518.3138
91.05310.3231-1.89962.773-0.74443.47430.1776-1.3695-0.05360.4487-0.6925-0.38030.6533-0.1969-0.60060.272-0.2595-0.06780.8488-0.10950.216618.545712.033927.1749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 293 through 318 )A293 - 318
2X-RAY DIFFRACTION2chain 'A' and (resid 319 through 337 )A319 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 399 )A338 - 399
4X-RAY DIFFRACTION4chain 'A' and (resid 400 through 420 )A400 - 420
5X-RAY DIFFRACTION5chain 'A' and (resid 421 through 461 )A421 - 461
6X-RAY DIFFRACTION6chain 'A' and (resid 462 through 484 )A462 - 484
7X-RAY DIFFRACTION7chain 'A' and (resid 485 through 527 )A485 - 527
8X-RAY DIFFRACTION8chain 'A' and (resid 528 through 550 )A528 - 550
9X-RAY DIFFRACTION9chain 'A' and (resid 551 through 570 )A551 - 570

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